An updated Axiom buffalo genotyping array map and mapping of cattle quantitative trait loci to the new water buffalo reference genome assembly

2021 ◽  
Author(s):  
A. V. Nascimento ◽  
A. R. S. Romero ◽  
M. Y. Nawaz ◽  
D. F. Cardoso ◽  
D. J. A. Santos ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Genome Assembly ◽  
Quantitative Trait ◽  
Water Buffalo ◽  
Reference Genome ◽  
Genotyping Array ◽  
Reference Genome Assembly ◽  
Trait Loci

scholarly journals Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing.

2020 ◽  
Author(s):  
Alia Parveen ◽  
Christa D. Jackson ◽  
Shatovisha Dey ◽  
Katy Tarrant ◽  
Nicholas B Anthony ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Genome Assembly ◽  
Quantitative Trait ◽  
Whole Genome ◽  
Chicken Chromosome ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Trait Loci ◽  
Whole Genome Resequencing ◽  
Ascites Syndrome

Abstract Background Ascites syndrome is a hypertensive, multifactorial, multigene trait affecting meat-type chickens imposing significant economic losses on the broiler industry. A region containing the CPQ gene has been previously identified as significantly affecting ascites phenotype. The region was discovered through whole genome resequencing focused on chicken chromosome 2. The association was confirmed through further genotyping in multiple broiler populations. Results The whole genome resequencing analyses have now been extended to the current chicken genome assembly. DNA samples were pooled according to gender and phenotype and the pools subjected to next generation sequencing. Loci were identified as clusters of single nucleotide polymorphisms where frequencies of the polymorphisms differed between resistant and susceptible chickens. The chickens are an unselected line descended from a commercial elite broiler line. Regions identified were specific to one or both genders. The data identify a total of 28 regions as potential quantitative trait loci for ascites. The genes from these regions have been associated with hypertensive-related traits in human association studies. One region on chicken chromosome 28 contains the LRRTM4 gene. Additional genotyping for the LRRTM4 region demonstrates an epistatic interaction with the CPQ region for ascites phenotype. Conclusions The 28 regions identified were not previously identified in a multi-generational genome wide association study using 60k Single Nucleotide Polymorphism panels. This work demonstrates the utility of whole genome resequencing as a cost effective, direct, and efficient method for identifying specific gene regions affecting complex traits. The approach is applicable to any organism with a genome assembly and requires no a priori assumptions.

scholarly journals Construction of a chromosome-level genome assembly for genome-wide identification of growth-related quantitative trait loci in Sinocyclocheilus grahami (Cypriniformes, Cyprinidae)

2021 ◽  
Vol 42 (3) ◽  
pp. 262-266
Author(s):  
Yan-Hui Yin ◽  
◽  
Xin-Hui Zhang ◽  
Xiao-Ai Wang ◽  
Rui-Han Li ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Genome Assembly ◽  
Quantitative Trait ◽  
Genome Wide ◽  
Trait Loci ◽  
Chromosome Level

scholarly journals Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing.

2020 ◽  
Author(s):  
Alia Parveen ◽  
Christa Jackson ◽  
Shatovisha Dey ◽  
Katy Tarrant ◽  
Nicholas B Anthony ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Genome Assembly ◽  
Quantitative Trait ◽  
Whole Genome ◽  
Chicken Chromosome ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Trait Loci ◽  
Whole Genome Resequencing ◽  
Ascites Syndrome

Abstract Background Ascites syndrome is a hypertensive, multifactorial, multigene trait affecting meat-type chickens imposing significant economic losses on the broiler industry. A region containing the CPQ gene has been previously identified as significantly affecting ascites phenotype. The region was discovered through whole genome resequencing focused on chicken chromosome 2. The association was confirmed through further genotyping in multiple broiler populations. Results The whole genome resequencing analyses have now been extended to the current chicken genome assembly. DNA samples were pooled according to gender and phenotype and the pools subjected to next generation sequencing. Loci were identified as clusters of single nucleotide polymorphisms where frequencies of the polymorphisms differed between resistant and susceptible chickens. The chickens are an unselected line descended from a commercial elite broiler line. Regions identified were specific to one or both genders. The data identify a total of 28 regions as potential quantitative trait loci for ascites. The genes from these regions have been associated with hypertensive-related traits in human association studies. One region on chicken chromosome 28 contains the LRRTM4 gene. Additional genotyping for the LRRTM4 region demonstrates an epistatic interaction with the CPQ region for ascites phenotype. Conclusions The 28 regions identified were not previously identified in a multi-generational genome wide association study using 60k Single Nucleotide Polymorphism panels. This work demonstrates the utility of whole genome resequencing as a cost effective, direct, and efficient method for identifying specific gene regions affecting complex traits. The approach is applicable to any organism with a genome assembly and requires no a priori assumptions.

Identification of cis-regulated genes in quantitative trait loci driving liver fibrosis

2012 ◽  
Vol 50 (08) ◽  
Author(s):  
R Hall ◽  
R Müllenbach ◽  
S Huss ◽  
R Alberts ◽  
K Schughart ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Liver Fibrosis ◽  
Quantitative Trait ◽  
Trait Loci

Identification of NASH Quantitative Trait Loci (QTLs) using in silico mapping analysis in inbred mice

2004 ◽  
Vol 42 (08) ◽  
Author(s):  
F Lammert ◽  
S Hillebrandt ◽  
S Matern ◽  
K Spatz ◽  
RM Green
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
In Silico ◽  
Inbred Mice ◽  
In Silico Mapping ◽  
Mapping Analysis ◽  
Trait Loci

Quantitative trait loci polymorphism in the reserve population of dual-purpose chickens

2018 ◽  
Vol 20 (4) ◽  
pp. 74-80
Author(s):  
L. V. Shulika ◽  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Dual Purpose ◽  
Trait Loci
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